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• 1. [Article] Juvenile coho salmon movement, growth and survival in a coastal basin of southern Oregon

  Juvenile salmonids display highly variable spatial and temporal movement patterns that are influenced by density dependent (e.g., competition, predation) and density independent (e.g., genetics, stream ...

  Citation × Citation Citation Abstract Copy Title: Juvenile coho salmon movement, growth and survival in a coastal basin of southern Oregon Author: Weybright, Adam D. Juvenile salmonids display highly variable spatial and temporal movement patterns that are influenced by density dependent (e.g., competition, predation) and density independent (e.g., genetics, stream discharge, physical habitat conditions) factors. The effects of these factors differ with fish life history stage, but will ultimately affect how salmonids utilize freshwater nursery habitats and influence their size at smolting. Although juvenile coho salmon (Oncorhynchus kisutch) (Walbaum 1792) movement patterns and their relationships with body mass have been previously examined, the temporal scale considered in most studies has been within individual seasonal periods. In this study, we monitored the movement of PIT tagged juvenile coho salmon throughout the period of freshwater residence in an entire southern Oregon coastal basin to identify the prevalent sedentary and mobile strategies these fish may adopt and to examine possible relationships between those strategies and fish body mass, growth and survival. Specific objectives include: 1) to describe juvenile coho salmon movement strategies and patterns during the freshwater residence period; 2) to determine the relative proportions of juvenile coho salmon that exhibit each movement strategy; 3) to establish whether juvenile coho salmon body mass and growth rates are related with a set of habitat variables recorded during this study; 4) to determine whether coho salmon body mass or growth rates are related to movement strategy; and 5) to evaluate whether winter survival of juvenile coho salmon is associated with movement strategy. Results revealed seasonally and spatially variable movement. More than half of coho salmon tracked throughout the period of freshwater residence exhibited movement behavior that differed between summer and winter seasons. Within seasonal periods, coho salmon in tidally affected reaches exhibited greater prevalence of mobile behavior relative to those in riverine reaches. Regression analysis indicated coho biomass density, habitat unit structural complexity and size at tagging were important in predicting summer growth of coho salmon. Juvenile coho salmon that were mobile during summer were either larger or no different in body mass in early summer relative to fish that exhibited sedentary behavior. Similarly, no consistent differences were observed between sedentary and mobile coho salmon in regards to summer growth. Coho salmon that were sedentary in summer and winter experienced higher apparent winter survival than mobile fish in each season, though the reach in which an individual resided at the start of winter appeared to also affect survival. Coho salmon residing in the tide gate reservoir reach and mainstem headwater reaches experienced greatest apparent winter survival. These results indicate that juvenile coho salmon movement within a stream basin is spatially and temporally variable and that mobility does not necessarily indicate inferior competitive ability. In a broader context, variable movement patterns reflect the capacity for plastic behavior in salmonids and this research demonstrates the importance of maintaining seasonally diverse freshwater and estuarine nursery habitats for juvenile fish. Title: Juvenile coho salmon movement, growth and survival in a coastal basin of southern Oregon Author: Weybright, Adam D. Juvenile salmonids display highly variable spatial and temporal movement patterns that are influenced by density dependent (e.g., competition, predation) and density independent (e.g., genetics, stream discharge, physical habitat conditions) factors. The effects of these factors differ with fish life history stage, but will ultimately affect how salmonids utilize freshwater nursery habitats and influence their size at smolting. Although juvenile coho salmon (Oncorhynchus kisutch) (Walbaum 1792) movement patterns and their relationships with body mass have been previously examined, the temporal scale considered in most studies has been within individual seasonal periods. In this study, we monitored the movement of PIT tagged juvenile coho salmon throughout the period of freshwater residence in an entire southern Oregon coastal basin to identify the prevalent sedentary and mobile strategies these fish may adopt and to examine possible relationships between those strategies and fish body mass, growth and survival. Specific objectives include: 1) to describe juvenile coho salmon movement strategies and patterns during the freshwater residence period; 2) to determine the relative proportions of juvenile coho salmon that exhibit each movement strategy; 3) to establish whether juvenile coho salmon body mass and growth rates are related with a set of habitat variables recorded during this study; 4) to determine whether coho salmon body mass or growth rates are related to movement strategy; and 5) to evaluate whether winter survival of juvenile coho salmon is associated with movement strategy. Results revealed seasonally and spatially variable movement. More than half of coho salmon tracked throughout the period of freshwater residence exhibited movement behavior that differed between summer and winter seasons. Within seasonal periods, coho salmon in tidally affected reaches exhibited greater prevalence of mobile behavior relative to those in riverine reaches. Regression analysis indicated coho biomass density, habitat unit structural complexity and size at tagging were important in predicting summer growth of coho salmon. Juvenile coho salmon that were mobile during summer were either larger or no different in body mass in early summer relative to fish that exhibited sedentary behavior. Similarly, no consistent differences were observed between sedentary and mobile coho salmon in regards to summer growth. Coho salmon that were sedentary in summer and winter experienced higher apparent winter survival than mobile fish in each season, though the reach in which an individual resided at the start of winter appeared to also affect survival. Coho salmon residing in the tide gate reservoir reach and mainstem headwater reaches experienced greatest apparent winter survival. These results indicate that juvenile coho salmon movement within a stream basin is spatially and temporally variable and that mobility does not necessarily indicate inferior competitive ability. In a broader context, variable movement patterns reflect the capacity for plastic behavior in salmonids and this research demonstrates the importance of maintaining seasonally diverse freshwater and estuarine nursery habitats for juvenile fish. Close

• 2. [Article] An Investigation of Ceratomyxa shasta sporulation following death of its Chinook salmon host

  As pre-spawning mortality (PSM) in Chinook salmon in the Willamette River Valley becomes a more defined and examined area of study, more focus is granted to not only preserving the health of these fish, ...

  Citation × Citation Citation Abstract Copy Title: An Investigation of Ceratomyxa shasta sporulation following death of its Chinook salmon host Author: Soderlund, Krista M. As pre-spawning mortality (PSM) in Chinook salmon in the Willamette River Valley becomes a more defined and examined area of study, more focus is granted to not only preserving the health of these fish, but also expanding knowledge concerning various pathogens that utilize the salmon as hosts and may be associated with PSM. One such parasite, a myxozoan named Ceratomyxa shasta, has been known to be extremely detrimental to salmon health, yet little literature exists concerning what exactly happens to this parasite once the salmon die. This thesis briefly outlines the complexity regarding this parasite’s relationship with the Chinook salmon, offers some context to transmission dynamics, and explores a recent investigation conducted over the course of the 2013-2014 academic year to determine the capability of Ceratomyxa shasta to live, continue to develop, and sporulate following the death of one of its hosts, the Chinook salmon. Title: An Investigation of Ceratomyxa shasta sporulation following death of its Chinook salmon host Author: Soderlund, Krista M. As pre-spawning mortality (PSM) in Chinook salmon in the Willamette River Valley becomes a more defined and examined area of study, more focus is granted to not only preserving the health of these fish, but also expanding knowledge concerning various pathogens that utilize the salmon as hosts and may be associated with PSM. One such parasite, a myxozoan named Ceratomyxa shasta, has been known to be extremely detrimental to salmon health, yet little literature exists concerning what exactly happens to this parasite once the salmon die. This thesis briefly outlines the complexity regarding this parasite’s relationship with the Chinook salmon, offers some context to transmission dynamics, and explores a recent investigation conducted over the course of the 2013-2014 academic year to determine the capability of Ceratomyxa shasta to live, continue to develop, and sporulate following the death of one of its hosts, the Chinook salmon. Close

• 3. [Article] Life histories of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Columbia River estuary as inferred from scale and otolith microchemistry

  Despite evidence that juvenile Chinook salmon (Oncorhynchus tshawytscha) utilize North Pacific estuaries for growth and salinity acclimation, research in the Columbia River estuary has lead to opposing ...

  Citation × Citation Citation Abstract Copy Title: Life histories of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Columbia River estuary as inferred from scale and otolith microchemistry Author: Campbell, Lance A. Despite evidence that juvenile Chinook salmon (Oncorhynchus tshawytscha) utilize North Pacific estuaries for growth and salinity acclimation, research in the Columbia River estuary has lead to opposing hypotheses about the estuary’s importance as a salmon rearing environment. Many contemporary tagging studies indicate that salmon residency within the estuary is short (< 1 week) and that mortality of estuarine migrants is a significant impediment to recovery of depressed salmon stocks. On the other hand, life history interpretations from fish scales collected early in the twentieth century suggest that juvenile Chinook salmon reared extensively in the estuary, leading some to hypothesize that life history variation has been constrained by anthropogenic changes in the Columbia River basin. To test these hypotheses we first validated previous methods of life history interpretation by comparing the results of otolith chemistry, scale chemistry, and scale morphology from juvenile salmon collected during monthly beach seine surveys in 2003. Although scale and otolith chemistry were strongly correlated, and scale chemistry was an accurate indicator of salt-water entry, scale morphometric characteristics did not coincide consistently with the time of salmon entry into brackish water. We measured Strontium 86 and Calcium 43 in salmon otoliths collected in the lower Columbia River estuary in 2003-05 to quantify the period of salt-water residency of juvenile salmon and to back-calculate their size at salt-water entry. The estimated salt-water residency of juvenile Chinook ranged from 0-176 days with a mean residence time of 54, 67 and 30 days in 2003, 2004 and 2005, respectively. Chinook salmon that resided in salt water for more than 30 days comprised 55, 51 and 30% of the total estuary beach seine collections during each of these years. Forty to fifty percent of Chinook salmon had entered the saline portion of the estuary at a fork length < 60 mm. Furthermore we found a negative relationship between the size and time of entry with residency, where smaller earlier migrants on average resided for longer periods then larger late migrants. Peak migration times occurred in May, and 90% of the outmigration was completed by August 30 in all years. This pattern is substantially truncated relative to the results of a 1914-1916 salmon life-history survey, which showed that the historical outmigration period lasted well into the fall and was characterized by late pulses of new recruits into the lower estuary. Nonetheless, recent otolith results indicate that subyearling Chinook salmon use the saline portion of the estuary in a high proportion and for extended periods of time in contrast to short residency times reported by contemporary tagging and marking studies. Title: Life histories of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Columbia River estuary as inferred from scale and otolith microchemistry Author: Campbell, Lance A. Despite evidence that juvenile Chinook salmon (Oncorhynchus tshawytscha) utilize North Pacific estuaries for growth and salinity acclimation, research in the Columbia River estuary has lead to opposing hypotheses about the estuary’s importance as a salmon rearing environment. Many contemporary tagging studies indicate that salmon residency within the estuary is short (< 1 week) and that mortality of estuarine migrants is a significant impediment to recovery of depressed salmon stocks. On the other hand, life history interpretations from fish scales collected early in the twentieth century suggest that juvenile Chinook salmon reared extensively in the estuary, leading some to hypothesize that life history variation has been constrained by anthropogenic changes in the Columbia River basin. To test these hypotheses we first validated previous methods of life history interpretation by comparing the results of otolith chemistry, scale chemistry, and scale morphology from juvenile salmon collected during monthly beach seine surveys in 2003. Although scale and otolith chemistry were strongly correlated, and scale chemistry was an accurate indicator of salt-water entry, scale morphometric characteristics did not coincide consistently with the time of salmon entry into brackish water. We measured Strontium 86 and Calcium 43 in salmon otoliths collected in the lower Columbia River estuary in 2003-05 to quantify the period of salt-water residency of juvenile salmon and to back-calculate their size at salt-water entry. The estimated salt-water residency of juvenile Chinook ranged from 0-176 days with a mean residence time of 54, 67 and 30 days in 2003, 2004 and 2005, respectively. Chinook salmon that resided in salt water for more than 30 days comprised 55, 51 and 30% of the total estuary beach seine collections during each of these years. Forty to fifty percent of Chinook salmon had entered the saline portion of the estuary at a fork length < 60 mm. Furthermore we found a negative relationship between the size and time of entry with residency, where smaller earlier migrants on average resided for longer periods then larger late migrants. Peak migration times occurred in May, and 90% of the outmigration was completed by August 30 in all years. This pattern is substantially truncated relative to the results of a 1914-1916 salmon life-history survey, which showed that the historical outmigration period lasted well into the fall and was characterized by late pulses of new recruits into the lower estuary. Nonetheless, recent otolith results indicate that subyearling Chinook salmon use the saline portion of the estuary in a high proportion and for extended periods of time in contrast to short residency times reported by contemporary tagging and marking studies. Close

• 4. [Article] Review of the hatchery measures in the Oregon plan for salmon and watersheds. Part I: consistency of the Oregon Plan with recommendations from recent scientific review panels

  This report was written by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds

  Citation × Citation Citation Abstract Copy Title: Review of the hatchery measures in the Oregon plan for salmon and watersheds. Part I: consistency of the Oregon Plan with recommendations from recent scientific review panels Author: Independent Multidisciplinary Science Team (Or.) This report was written by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds Title: Review of the hatchery measures in the Oregon plan for salmon and watersheds. Part I: consistency of the Oregon Plan with recommendations from recent scientific review panels Author: Independent Multidisciplinary Science Team (Or.) This report was written by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds Close

• 5. [Article] Variation in the timing of coho salmon (Oncorhynchus kisutch) migration and spawning relative to river discharge and temperature

  Coho salmon (Oncorhynchus kisutch) migration and spawning are unique components of the salmon life cycle because they require synchrony of behavior with other individuals as well as with acceptable fluvial ...

  Citation × Citation Citation Abstract Copy Title: Variation in the timing of coho salmon (Oncorhynchus kisutch) migration and spawning relative to river discharge and temperature Author: LovellFord, Rachel Coho salmon (Oncorhynchus kisutch) migration and spawning are unique components of the salmon life cycle because they require synchrony of behavior with other individuals as well as with acceptable fluvial conditions. As with other organisms that exhibit group mating behavior, it is likely that environmental cues trigger coho salmon movement to spawning grounds. These cues may also provide usable habitat for migration and spawning. River discharge, temperature, and length of day have long been assumed to be the environmental cues which trigger migration and spawning of coho salmon as coho return within the same season each year to spawn. Hatchery studies have also shown that the timing of reproductive behavior is heritable. If this heritability is determined by the fluvial conditions of the spawning grounds, then a predictable relationship should exist between reproductive behavior and the hydrologic and thermal regimes. Surprisingly, no defensible correlations between discharge thresholds and spawning or migrating activity have been identified for naturally reproducing coho salmon. Thermal, velocity, and depth limitations have been identified for coho salmon, but these values have not been examined in combination or within the context of a hydrologic and thermal regime. This study compares interannual patterns in the timing of coho mid-river migration in the North Umqua (180 km up river from the estuary) and the initiation of spawn timing in the Smith River basins (Oregon) with river discharge and water temperature data to ascertain whether these behaviors are driven by fluvial conditions. Additionally, we used this data to identify the window over which most migration and spawning takes place in our test systems. On the North Umpqua, coho salmon mid-river migration initiated (first 5% of migrants) after summer peak temperatures and following a threshold average daily temperature of 18 C°, but before fall storm events occurred. In most years, approximately 75% of the migrating coho salmon have moved past the Winchester Dam before fall storms initiated and when discharge remained less than the 11 year average for the month of November, more similar to summer than winter flow levels. Additionally, characteristic lengths and numbers of peaks within the distribution of annual migrations were attributable to the generational cohort that the migration belonged to despite the similarity in population size across all years. These patterns in the distribution of generational cohorts suggest an inherited timing response as well as highlight cohorts which may contain diminished sub-populations. The initiation of coho salmon spawning appears limited both by a thermal threshold of 12 C° in all basins, as well as by a minimal discharge threshold, which is unique to each stream. Continued spawning activity occurs as discharge remains elevated from fall levels. It is also notable that there was no statistical difference in the date of the initiation of spawning within each basin in a given year or across years at a given site. Together, these studies highlight the important role that the coho salmon genome plays in reproductive timing as well as the ways that fluvial thresholds limit reproductive behavior in time. Coho have survived because of their genome has been resilient when faced with environmental change. Future work should consider variability in fluvial conditions relative to coho salmon phenotypic plasticity over time. Coho salmon phenotypic plasticity will determine whether the rate of change of the hydrologic and thermal regimes important to coho salmon survival outpaces the coho’s ability to adapt. This study contributed to this future work by establishing baseline relationships between the behavior of a threatened species and measurable environmental thresholds. Title: Variation in the timing of coho salmon (Oncorhynchus kisutch) migration and spawning relative to river discharge and temperature Author: LovellFord, Rachel Coho salmon (Oncorhynchus kisutch) migration and spawning are unique components of the salmon life cycle because they require synchrony of behavior with other individuals as well as with acceptable fluvial conditions. As with other organisms that exhibit group mating behavior, it is likely that environmental cues trigger coho salmon movement to spawning grounds. These cues may also provide usable habitat for migration and spawning. River discharge, temperature, and length of day have long been assumed to be the environmental cues which trigger migration and spawning of coho salmon as coho return within the same season each year to spawn. Hatchery studies have also shown that the timing of reproductive behavior is heritable. If this heritability is determined by the fluvial conditions of the spawning grounds, then a predictable relationship should exist between reproductive behavior and the hydrologic and thermal regimes. Surprisingly, no defensible correlations between discharge thresholds and spawning or migrating activity have been identified for naturally reproducing coho salmon. Thermal, velocity, and depth limitations have been identified for coho salmon, but these values have not been examined in combination or within the context of a hydrologic and thermal regime. This study compares interannual patterns in the timing of coho mid-river migration in the North Umqua (180 km up river from the estuary) and the initiation of spawn timing in the Smith River basins (Oregon) with river discharge and water temperature data to ascertain whether these behaviors are driven by fluvial conditions. Additionally, we used this data to identify the window over which most migration and spawning takes place in our test systems. On the North Umpqua, coho salmon mid-river migration initiated (first 5% of migrants) after summer peak temperatures and following a threshold average daily temperature of 18 C°, but before fall storm events occurred. In most years, approximately 75% of the migrating coho salmon have moved past the Winchester Dam before fall storms initiated and when discharge remained less than the 11 year average for the month of November, more similar to summer than winter flow levels. Additionally, characteristic lengths and numbers of peaks within the distribution of annual migrations were attributable to the generational cohort that the migration belonged to despite the similarity in population size across all years. These patterns in the distribution of generational cohorts suggest an inherited timing response as well as highlight cohorts which may contain diminished sub-populations. The initiation of coho salmon spawning appears limited both by a thermal threshold of 12 C° in all basins, as well as by a minimal discharge threshold, which is unique to each stream. Continued spawning activity occurs as discharge remains elevated from fall levels. It is also notable that there was no statistical difference in the date of the initiation of spawning within each basin in a given year or across years at a given site. Together, these studies highlight the important role that the coho salmon genome plays in reproductive timing as well as the ways that fluvial thresholds limit reproductive behavior in time. Coho have survived because of their genome has been resilient when faced with environmental change. Future work should consider variability in fluvial conditions relative to coho salmon phenotypic plasticity over time. Coho salmon phenotypic plasticity will determine whether the rate of change of the hydrologic and thermal regimes important to coho salmon survival outpaces the coho’s ability to adapt. This study contributed to this future work by establishing baseline relationships between the behavior of a threatened species and measurable environmental thresholds. Close

• 6. [Article] Tags Versus Genetics : Identifying Which Tool Provides the Best Information about Chinook Salmon (Oncorhynchus tshawytscha) Distributions in the California Current

  The movement of Chinook salmon through space and time, across political boundaries, and through fisheries, creates one of the most complex marine resource management problems in the world. Information ...

  Citation × Citation Citation Abstract Copy Title: Tags Versus Genetics : Identifying Which Tool Provides the Best Information about Chinook Salmon (Oncorhynchus tshawytscha) Distributions in the California Current Author: Flaherty, Ryan James The movement of Chinook salmon through space and time, across political boundaries, and through fisheries, creates one of the most complex marine resource management problems in the world. Information garnered from the recovery of coded-wire tags (CWTs) has been used since the 1970s to direct management decisions. Growing concern surrounding the quality and limitations of CWT data spurred interest in technologies that may improve stock specific information for Chinook salmon. Genetic stock identification (GSI) is one of the rapidly growing technologies with significant potential for generating information that could be used in addition to CWT data to improve salmon management. This is the first study to explicitly compare the capabilities of CWT and GSI data to identify stock-specific distribution patterns of Chinook salmon. Our results demonstrate that GSI data are a powerful tool that can be used to investigate stock-specific Chinook distributions at refined space-time scales that cannot be investigated with traditionally reported CWT data. Additionally, we found that, at coarse space-time scales, CWT and GSI data provide similar stock distribution information, lending support to the critical assumption that CWT data reflect the distribution patterns of the untagged fish they are intended to represent. As a by-product of this comparison, we describe the distribution and migration patterns of the Chinook stocks most commonly encountered in the commercial fishery off the coasts of Oregon and California. GSI and other 21st century genetics-based tools have potential to play a critical role in improving salmon management regimes of the future. Title: Tags Versus Genetics : Identifying Which Tool Provides the Best Information about Chinook Salmon (Oncorhynchus tshawytscha) Distributions in the California Current Author: Flaherty, Ryan James The movement of Chinook salmon through space and time, across political boundaries, and through fisheries, creates one of the most complex marine resource management problems in the world. Information garnered from the recovery of coded-wire tags (CWTs) has been used since the 1970s to direct management decisions. Growing concern surrounding the quality and limitations of CWT data spurred interest in technologies that may improve stock specific information for Chinook salmon. Genetic stock identification (GSI) is one of the rapidly growing technologies with significant potential for generating information that could be used in addition to CWT data to improve salmon management. This is the first study to explicitly compare the capabilities of CWT and GSI data to identify stock-specific distribution patterns of Chinook salmon. Our results demonstrate that GSI data are a powerful tool that can be used to investigate stock-specific Chinook distributions at refined space-time scales that cannot be investigated with traditionally reported CWT data. Additionally, we found that, at coarse space-time scales, CWT and GSI data provide similar stock distribution information, lending support to the critical assumption that CWT data reflect the distribution patterns of the untagged fish they are intended to represent. As a by-product of this comparison, we describe the distribution and migration patterns of the Chinook stocks most commonly encountered in the commercial fishery off the coasts of Oregon and California. GSI and other 21st century genetics-based tools have potential to play a critical role in improving salmon management regimes of the future. Close

• 7. [Article] The Scientific Basis for Artificial Propagation in the Recovery of Wild Anadromous Salmonids in Oregon

  This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds

  Citation × Citation Citation Abstract Copy Title: The Scientific Basis for Artificial Propagation in the Recovery of Wild Anadromous Salmonids in Oregon Author: Independent Multidisciplinary Science Team (Or.) This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds Title: The Scientific Basis for Artificial Propagation in the Recovery of Wild Anadromous Salmonids in Oregon Author: Independent Multidisciplinary Science Team (Or.) This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds Close

• 8. [Article] The Salmon-Agreement between Norway and EU - A Welfare Economic Analysis

  Research Paper

  Citation × Citation Citation Abstract Copy Title: The Salmon-Agreement between Norway and EU - A Welfare Economic Analysis Author: Lorentzen, Torbjorn Research Paper Title: The Salmon-Agreement between Norway and EU - A Welfare Economic Analysis Author: Lorentzen, Torbjorn Research Paper Close

• 9. [Article] 1999-1.pdf

  Citation × Citation Citation Abstract Copy Title: 1999-1.pdf Author: Independent Multidisciplinary Science Team (Or.) Title: 1999-1.pdf Author: Independent Multidisciplinary Science Team (Or.) Close

• 10. [Article] 1999-1add.pdf

  Citation × Citation Citation Abstract Copy Title: 1999-1add.pdf Author: Independent Multidisciplinary Science Team (Or.) Title: 1999-1add.pdf Author: Independent Multidisciplinary Science Team (Or.) Close